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  • Split paired end multi-sample fastq to single-sample fastq

    Hi,

    I have a single, multi-sample FASTQ file containing paired end reads from dozens of samples. I would like to split this file into individual sample-level FASTQ files.

    Code:
    @SRR0000001.1.1 HISCAN01_77:4:1104:20579:289221 length=100
    GCTGGA
    +SRR0000001.1.1 HISCAN01_77:4:1104:20579:289221 length=100
    @@<BDDAD;A<<CC+2AEFFBFH>EG###########
    @SRR0000001.1.2 HISCAN01_77:4:1104:20579:289221 length=100
    GCTCTA
    +SRR0000001.1.2 HISCAN01_77:4:1104:20579:289221 length=100
    B?;DDBD;8DD))
    @SRR0000002.2.1 HISCAN01_61:2:2204:29774:93471 length=100
    GCTTGC
    +SRR0000002.2.1 HISCAN01_61:2:2204:29774:93471 length=100
    BCCFFFFFFHHHHJJJJJJJJJJJJ:ACDD9AACDD
    I would like to split this file into the following files:

    Code:
    SRR0000001_1.fastq
    SRR0000001_2.fastq
    SRR0000002_1.fastq
    SRR0000002_2.fastq
    SRR0000003_1.fastq
    SRR0000003_2.fastq
    I would appreciate your help.

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